The native structure of the lattice trefoil (protein K) explored in this study.

<p>In panel (A) we show the three-dimensional representation and in (B) the contact map representation. In (A) the minimal chain segment that contains the knot, extending from bead 3 to bead 22, is highlighted. Bead 1, representing the C-terminus, is colored red and the N-terminus is colored blue. In (B) the 8 native contacts that are established between the residues that make up the knotted core is highlighted. Panels (C) and (D) represent the native structure and contact map of the unknotted lattice protein. In (E) we illustrate the folding setup where the C-terminus is linked to an inert plane by a linker whose size is one-lattice spacing. The trefoil symbol is used to indicate that conformation K is knotted and the circle is used to indicate that conformation U is unknotted.